roms-tools 3.0.0__py3-none-any.whl → 3.1.1__py3-none-any.whl

roms_tools/setup/utils.py

@@ -1,9 +1,11 @@
 import importlib.metadata
+import logging
+from collections.abc import Sequence
 from dataclasses import asdict, fields, is_dataclass
 from datetime import datetime
 from enum import StrEnum
 from pathlib import Path
-from typing import Any, Dict, Sequence, Type, Union
+from typing import Any
 
 import cftime
 import numba as nb
@@ -47,7 +49,6 @@ def nan_check(field, mask, error_message=None) -> None:
         If the field contains NaN values at any of the wet points indicated by the mask.
         The error message will explain the potential cause and suggest ensuring the dataset's coverage.
     """
-
     # Replace values in field with 0 where mask is not 1
     da = xr.where(mask == 1, field, 0)
     if error_message is None:
@@ -78,7 +79,6 @@ def substitute_nans_by_fillvalue(field, fill_value=0.0) -> xr.DataArray:
     xr.DataArray
         The data array with NaN values replaced by the specified fill value.
     """
-
     return field.fillna(fill_value)
 
 
@@ -139,9 +139,7 @@ def assign_dates_to_climatology(ds: xr.Dataset, time_dim: str) -> xr.Dataset:
 def interpolate_cyclic_time(
     data_array: xr.DataArray,
     time_dim_name: str,
-    day_of_year: Union[
-        int, float, np.ndarray, xr.DataArray, Sequence[Union[int, float]]
-    ],
+    day_of_year: int | float | np.ndarray | xr.DataArray | Sequence[int | float],
 ) -> xr.DataArray:
     """Interpolates a DataArray cyclically across the start and end of the year.
 
@@ -173,7 +171,6 @@ def interpolate_cyclic_time(
       represents a repeating annual cycle.
     - The `day_of_year` values should be within the range [1, 365] or [1, 366] for leap years.
     """
-
     # Concatenate across the beginning and end of the year
     time_concat = xr.concat(
         [
@@ -205,10 +202,10 @@ def interpolate_cyclic_time(
 
 
 def interpolate_from_climatology(
-    field: Union[xr.DataArray, xr.Dataset],
+    field: xr.DataArray | xr.Dataset,
     time_dim_name: str,
-    time: Union[xr.DataArray, pd.DatetimeIndex],
-) -> Union[xr.DataArray, xr.Dataset]:
+    time: xr.DataArray | pd.DatetimeIndex,
+) -> xr.DataArray | xr.Dataset:
     """Interpolates a climatological field to specified time points.
 
     This function interpolates the input `field` based on `day_of_year` values
@@ -241,7 +238,6 @@ def interpolate_from_climatology(
     """
 
     def interpolate_single_field(data_array: xr.DataArray) -> xr.DataArray:
-
         if isinstance(time, xr.DataArray):
             # Extract day of year from xarray.DataArray
             day_of_year = time.dt.dayofyear
@@ -318,7 +314,7 @@ def get_time_type(data_array: xr.DataArray) -> str:
     )
 
     # Check if any of the coordinate values are of cftime, datetime, or integer type
-    if isinstance(data_array.values, (np.ndarray, list)):
+    if isinstance(data_array.values, np.ndarray | list):
         # Check if the data type is numpy datetime64, indicating standard datetime objects
         if data_array.values.dtype == "datetime64[ns]":
             return "datetime"
@@ -385,7 +381,6 @@ def get_variable_metadata():
     dict of str: dict
         Dictionary where keys are variable names and values are dictionaries with "long_name" and "units" keys.
     """
-
     d = {
         "ssh_Re": {"long_name": "Tidal elevation, real part", "units": "m"},
         "ssh_Im": {"long_name": "Tidal elevation, complex part", "units": "m"},
@@ -639,7 +634,6 @@ def compute_missing_bgc_variables(bgc_data):
       dictionary, they are filled with constant values.
     - `CHL` is removed from the dictionary after the necessary calculations.
     """
-
     # Define the relationships for missing variables
     variable_relations = {
         "NH4": (None, 10**-6),  # mmol m-3
@@ -708,7 +702,6 @@ def compute_missing_surface_bgc_variables(bgc_data):
     -----
     - If `nox` and `nhy` are not part of the input dictionary, the are assigned constant values.
     """
-
     # Define the relationships for missing variables
     variable_relations = {
         "pco2_air_alt": ("pco2_air", 1.0),
@@ -947,7 +940,6 @@ def group_dataset(ds, filepath):
     tuple
         A tuple containing the list of grouped datasets and corresponding output filenames.
     """
-
     if hasattr(ds, "climatology"):
         output_filename = f"{filepath}_clim"
         output_filenames = [output_filename]
@@ -1000,7 +992,6 @@ def group_by_month(ds, filepath):
     tuple
         A tuple containing the list of monthly datasets and corresponding output filenames.
     """
-
     dataset_list = []
     output_filenames = []
 
@@ -1037,7 +1028,6 @@ def group_by_year(ds, filepath):
     tuple
         A tuple containing the list of yearly datasets and corresponding output filenames.
     """
-
     dataset_list = []
     output_filenames = []
 
@@ -1151,7 +1141,6 @@ def rotate_velocities(
       - u_rot = u * cos(angle) + v * sin(angle)
       - v_rot = v * cos(angle) - u * sin(angle)
     """
-
     # Rotate velocities to grid orientation
     u_rot = u * np.cos(angle) + v * np.sin(angle)
     v_rot = v * np.cos(angle) - u * np.sin(angle)
@@ -1188,7 +1177,6 @@ def compute_barotropic_velocity(
     Computed as:
       - `vel_bar` = sum(dz * vel) / sum(dz)
     """
-
     # Layer thickness
     dz = -interface_depth.diff(dim="s_w")
     dz = dz.rename({"s_w": "s_rho"})
@@ -1356,7 +1344,6 @@ def min_dist_to_land(
     2-D Array of the same shape as lon and lat, which will be filled with the resulting distance values
     to the nearest non-nan lon2, lat2 point
     """
-
     # get flattened ocean/land indices
     ocean = (mask == 1).ravel()
     land = (mask == 0).ravel()
@@ -1387,8 +1374,8 @@ def min_dist_to_land(
 
 
 def convert_to_relative_days(
-    times: Union[Sequence[datetime], np.ndarray],
-    model_reference_date: Union[datetime, np.datetime64],
+    times: Sequence[datetime] | np.ndarray,
+    model_reference_date: datetime | np.datetime64,
 ) -> np.ndarray:
     """Convert absolute datetimes to model-relative time in days.
 
@@ -1413,7 +1400,7 @@ def convert_to_relative_days(
 
 def add_time_info_to_ds(
     ds: xr.Dataset,
-    model_reference_date: Union[datetime, np.datetime64],
+    model_reference_date: datetime | np.datetime64,
     climatology: bool,
     time_name: str = "time",
 ) -> tuple[xr.Dataset, xr.DataArray]:
@@ -1435,7 +1422,6 @@ def add_time_info_to_ds(
     tuple[xr.Dataset, xr.DataArray]
         Updated dataset with time information and the relative time array.
     """
-
     if climatology:
         ds.attrs["climatology"] = str(True)
         month = xr.DataArray(range(1, 13), dims=time_name)
@@ -1469,7 +1455,7 @@ def add_time_info_to_ds(
     abs_time.attrs["long_name"] = "absolute time"
     ds = ds.assign_coords({"abs_time": abs_time})
 
-    time.attrs["long_name"] = f"relative time: days since {str(model_reference_date)}"
+    time.attrs["long_name"] = f"relative time: days since {model_reference_date!s}"
     time.encoding["units"] = "days"
     time.attrs["units"] = "days"
     ds.encoding["unlimited_dims"] = time_name
@@ -1482,7 +1468,7 @@ class NoAliasDumper(yaml.SafeDumper):
         return True
 
 
-def _write_to_yaml(yaml_data, filepath: Union[str, Path]) -> None:
+def write_to_yaml(yaml_data, filepath: str | Path) -> None:
     """Write pre-serialized YAML data and additional metadata to a YAML file.
 
     This function writes the provided pre-serialized YAML data along with metadata, such as the version
@@ -1501,7 +1487,6 @@ def _write_to_yaml(yaml_data, filepath: Union[str, Path]) -> None:
     None
         This function does not return anything. It writes the provided YAML data directly to the specified file.
     """
-
     # Convert the filepath to a Path object
     filepath = Path(filepath)
 
@@ -1527,7 +1512,7 @@ def _write_to_yaml(yaml_data, filepath: Union[str, Path]) -> None:
         )
 
 
-def _to_dict(forcing_object) -> dict:
+def to_dict(forcing_object, exclude: list[str] | None = None) -> dict:
     """Serialize a forcing object (including its grid) into a dictionary.
 
     This function serializes a dataclass object (forcing_object) and its associated
@@ -1542,19 +1527,20 @@ def _to_dict(forcing_object) -> dict:
     forcing_object : object
         The object that contains the forcing data, typically a dataclass with attributes
         such as `grid`, `start_time`, `end_time`, etc.
+    exclude : list[str], optional
+        List of keys to exclude from the serialized output. Defaults to empty list. The field "ds" is always excluded by default.
 
     Returns
     -------
     dict
     """
-
     # Serialize Grid data
     if hasattr(forcing_object, "grid") and forcing_object.grid is not None:
         grid_data = asdict(forcing_object.grid)
-        grid_yaml_data = {"Grid": _pop_grid_data(grid_data)}
+        grid_yaml_data = {"Grid": pop_grid_data(grid_data)}
     elif hasattr(forcing_object, "parent_grid"):
         grid_data = asdict(forcing_object.parent_grid)
-        grid_yaml_data = {"ParentGrid": _pop_grid_data(grid_data)}
+        grid_yaml_data = {"ParentGrid": pop_grid_data(grid_data)}
 
     # Ensure Paths are Strings
     def ensure_paths_are_strings(obj, key):
@@ -1581,20 +1567,11 @@ def _to_dict(forcing_object) -> dict:
     else:
         raise TypeError("Forcing object is not a dataclass or pydantic model")
 
-    filtered_field_names = [
-        param
-        for param in field_names
-        if param
-        not in (
-            "grid",
-            "parent_grid",
-            "ds",
-            "use_dask",
-            "climatology",
-            "verbose",
-            "straddle",
-        )
-    ]
+    if exclude is None:
+        exclude = []
+    exclude = ["grid", "parent_grid", "ds", *exclude]
+
+    filtered_field_names = [param for param in field_names if param not in exclude]
 
     for field_name in filtered_field_names:
         # Retrieve the value of each field using getattr
@@ -1619,7 +1596,7 @@ def _to_dict(forcing_object) -> dict:
     return yaml_data
 
 
-def _pop_grid_data(grid_data):
+def pop_grid_data(grid_data):
     grid_data.pop("ds", None)  # Remove 'ds' attribute (non-serializable)
     grid_data.pop("straddle", None)
     grid_data.pop("verbose", None)
@@ -1627,7 +1604,7 @@ def _pop_grid_data(grid_data):
     return grid_data
 
 
-def _from_yaml(forcing_object: Type, filepath: Union[str, Path]) -> Dict[str, Any]:
+def from_yaml(forcing_object: type, filepath: str | Path) -> dict[str, Any]:
     """Extract the configuration data for a given forcing object from a YAML file.
 
     This function reads a YAML file, searches for the configuration data associated
@@ -1714,7 +1691,6 @@ def handle_boundaries(field):
     field : numpy.ndarray or xarray.DataArray
         The input field with adjusted boundary values.
     """
-
     field[0, :] = field[1, :]
     field[-1, :] = field[-2, :]
     field[:, 0] = field[:, 1]
@@ -1741,7 +1717,6 @@ def get_boundary_coords():
           - "v" variables (e.g., `eta_v`)
           - "vector" variables with lists of indices for multiple grid points (e.g., `eta_rho`, `xi_rho`).
     """
-
     bdry_coords = {
         "rho": {
             "south": {"eta_rho": 0},
@@ -1820,3 +1795,59 @@ def to_float(val):
     if isinstance(val, list):
         return [float(v) for v in val]
     return float(val)
+
+
+def validate_names(
+    names: list[str] | str,
+    valid_names: list[str],
+    include_all_sentinel: str,
+    max_to_plot: int,
+    label: str = "item",
+) -> list[str]:
+    """
+    Generic validation and filtering for a list of names.
+
+    Parameters
+    ----------
+    names : list of str or sentinel
+        Names to validate, or sentinel value to include all valid names.
+    valid_names : list of str
+        List of valid names to check against.
+    include_all_sentinel : str
+        Sentinel value to indicate all names should be included.
+    max_to_plot : int
+        Maximum number of names to return.
+    label : str, default "item"
+        Label to use in error and warning messages.
+
+    Returns
+    -------
+    list of str
+        Validated and possibly truncated list of names.
+
+    Raises
+    ------
+    ValueError
+        If any names are invalid or input is not a list of strings.
+    """
+    if names == include_all_sentinel:
+        names = valid_names
+
+    if isinstance(names, list):
+        if not all(isinstance(n, str) for n in names):
+            raise ValueError(f"All elements in `{label}_names` must be strings.")
+    else:
+        raise ValueError(f"`{label}_names` should be a list of strings.")
+
+    invalid = [n for n in names if n not in valid_names]
+    if invalid:
+        raise ValueError(f"Invalid {label}s: {', '.join(invalid)}")
+
+    if len(names) > max_to_plot:
+        logging.warning(
+            f"Only the first {max_to_plot} {label}s will be plotted "
+            f"(received {len(names)})."
+        )
+        names = names[:max_to_plot]
+
+    return names

roms_tools/tests/test_analysis/test_roms_output.py

@@ -19,7 +19,6 @@ except ImportError:
 
 @pytest.fixture
 def roms_output_from_restart_file(use_dask):
-
     fname_grid = Path(download_test_data("epac25km_grd.nc"))
     grid = Grid.from_file(fname_grid)
 
@@ -33,7 +32,6 @@ def roms_output_from_restart_file(use_dask):
 
 @pytest.fixture
 def roms_output_from_restart_file_adjusted_for_zeta(use_dask):
-
     fname_grid = Path(download_test_data("epac25km_grd.nc"))
     grid = Grid.from_file(fname_grid)
 
@@ -48,7 +46,6 @@ def roms_output_from_restart_file_adjusted_for_zeta(use_dask):
 
 @pytest.fixture
 def roms_output_from_restart_file_with_straddling_grid(use_dask):
-
     # Make fake grid that straddles the dateline and that has consistent sizes with test data below
     grid = Grid(
         nx=8, ny=13, center_lon=0, center_lat=60, rot=32, size_x=244, size_y=365
@@ -216,7 +213,8 @@ def test_compute_depth_coordinates(use_dask):
 
 def test_missing_zeta_gets_raised(use_dask):
     """Test that a ValueError is raised when `zeta` is missing from the dataset and
-    `adjust_depth_for_sea_surface_height` is enabled."""
+    `adjust_depth_for_sea_surface_height` is enabled.
+    """
     # Load the grid
     fname_grid = Path(download_test_data("epac25km_grd.nc"))
     grid = Grid.from_file(fname_grid)
@@ -296,7 +294,6 @@ def test_plot_on_native_model_grid(roms_output_fixture, request):
 
     for include_boundary in [False, True]:
         for depth_contours in [False, True]:
-
             # 3D fields
             for var_name in ["temp", "u", "v"]:
                 kwargs = {
@@ -379,7 +376,6 @@ def test_plot_on_lat_lon(roms_output_fixture, lat, lon, request):
 
     for include_boundary in [False, True]:
         for depth_contours in [False, True]:
-
             # 3D fields
             for var_name in ["temp", "u", "v"]:
                 kwargs = {
@@ -449,7 +445,6 @@ def test_plot_on_lat_lon(roms_output_fixture, lat, lon, request):
 
 def test_plot_errors(roms_output_from_restart_file):
     """Test error conditions for the ROMSOutput.plot() method."""
-
     # Invalid time index
     with pytest.raises(ValueError, match="Invalid time index"):
         roms_output_from_restart_file.plot("temp", time=10, s=-1)
@@ -521,7 +516,6 @@ def test_plot_errors(roms_output_from_restart_file):
 
 
 def test_figure_gets_saved(roms_output_from_restart_file, tmp_path):
-
     filename = tmp_path / "figure.png"
     roms_output_from_restart_file.plot("temp", time=0, depth=1000, save_path=filename)
 

roms_tools/tests/test_regrid.py

@@ -16,8 +16,8 @@ from roms_tools.regrid import LateralRegridFromROMS
 @pytest.mark.skipif(xesmf is None, reason="xesmf required")
 def test_lateral_regrid_with_curvilinear_grid():
     """Test that LateralRegridFromROMS regrids data correctly from a curvilinear ROMS
-    grid."""
-
+    grid.
+    """
     # Define ROMS curvilinear grid dimensions
     eta_rho, xi_rho = 10, 20
 
@@ -57,7 +57,6 @@ def test_lateral_regrid_with_curvilinear_grid():
 @pytest.mark.skipif(xesmf is not None, reason="xesmf has to be missing")
 def test_lateral_regrid_import_error():
     """Test that LateralRegridFromROMS raises ImportError when xesmf is missing."""
-
     # Define mock ROMS curvilinear grid dimensions
     eta_rho, xi_rho = 10, 20
 
@@ -119,7 +118,6 @@ def vertical_regridder(depth_values, layer_depth_rho_values):
     ],
 )
 def test_vertical_regrid(request, depth_values, layer_depth_rho_values, temp_data):
-
     vertical_regrid = vertical_regridder(
         depth_values=depth_values, layer_depth_rho_values=layer_depth_rho_values
     )

roms_tools/tests/test_setup/test_boundary_forcing.py

@@ -24,7 +24,6 @@ from roms_tools.download import download_test_data
 )
 def test_boundary_forcing_creation(boundary_forcing_fixture, request):
     """Test the creation of the BoundaryForcing object."""
-
     boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     fname1 = Path(download_test_data("GLORYS_NA_20120101.nc"))
@@ -63,8 +62,8 @@ def test_boundary_forcing_creation_with_duplicates(
     boundary_forcing: BoundaryForcing, use_dask: bool
 ) -> None:
     """Test the creation of the BoundaryForcing object with duplicates in source data
-    works as expected."""
-
+    works as expected.
+    """
     fname1 = Path(download_test_data("GLORYS_NA_20120101.nc"))
     fname2 = Path(download_test_data("GLORYS_NA_20121231.nc"))
 
@@ -91,7 +90,6 @@ def test_boundary_forcing_creation_with_duplicates(
 )
 def test_bgc_boundary_forcing_creation(boundary_forcing_fixture, request):
     """Test the creation of the BoundaryForcing object."""
-
     boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     assert boundary_forcing.start_time == datetime(2021, 6, 29)
@@ -150,7 +148,6 @@ def test_bgc_boundary_forcing_creation(boundary_forcing_fixture, request):
 
 
 def test_unsuccessful_boundary_forcing_creation_with_1d_fill(use_dask):
-
     grid = Grid(
         nx=2,
         ny=2,
@@ -168,7 +165,6 @@ def test_unsuccessful_boundary_forcing_creation_with_1d_fill(use_dask):
     fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
 
     with pytest.raises(ValueError, match="consists entirely of NaNs"):
-
         BoundaryForcing(
             grid=grid,
             start_time=datetime(2021, 6, 29),
@@ -181,7 +177,6 @@ def test_unsuccessful_boundary_forcing_creation_with_1d_fill(use_dask):
     fname_bgc = download_test_data("CESM_regional_coarse_test_data_climatology.nc")
 
     with pytest.raises(ValueError, match="consists entirely of NaNs"):
-
         BoundaryForcing(
             grid=grid,
             start_time=datetime(2021, 6, 29),
@@ -257,7 +252,6 @@ def test_start_time_end_time_warning(use_dask, caplog):
 
 
 def test_boundary_divided_by_land_warning(caplog, use_dask):
-
     # Iceland intersects the western boundary of the following grid
     grid = Grid(
         nx=5, ny=5, size_x=500, size_y=500, center_lon=-10, center_lat=65, rot=0
@@ -279,7 +273,6 @@ def test_boundary_divided_by_land_warning(caplog, use_dask):
 
 
 def test_info_depth(caplog, use_dask):
-
     grid = Grid(
         nx=3,
         ny=3,
@@ -314,7 +307,6 @@ def test_info_depth(caplog, use_dask):
     caplog.clear()
 
     with caplog.at_level(logging.INFO):
-
         BoundaryForcing(
             grid=grid,
             start_time=datetime(2012, 1, 1),
@@ -331,7 +323,6 @@ def test_info_depth(caplog, use_dask):
 
 
 def test_info_fill(caplog, use_dask):
-
     grid = Grid(
         nx=3,
         ny=3,
@@ -369,7 +360,6 @@ def test_info_fill(caplog, use_dask):
     caplog.clear()
 
     with caplog.at_level(logging.INFO):
-
         BoundaryForcing(
             grid=grid,
             start_time=datetime(2012, 1, 1),
@@ -384,7 +374,6 @@ def test_info_fill(caplog, use_dask):
 
 
 def test_1d_and_2d_fill_coincide_if_no_fill(use_dask):
-
     grid = Grid(
         nx=2,
         ny=2,
@@ -424,7 +413,6 @@ def test_1d_and_2d_fill_coincide_if_no_fill(use_dask):
 
 
 def test_1d_and_2d_fill_coincide_if_no_land(use_dask):
-
     # this grid lies entirely over open ocean
     grid = Grid(nx=5, ny=5, size_x=300, size_y=300, center_lon=-5, center_lat=65, rot=0)
 
@@ -460,11 +448,9 @@ def test_1d_and_2d_fill_coincide_if_no_land(use_dask):
 def test_correct_depth_coords_adjusted_for_zeta(
     boundary_forcing_fixture, request, use_dask
 ):
-
     boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     for direction in ["south", "east", "north", "west"]:
-
         # Test that uppermost interface coincides with sea surface height
         assert np.allclose(
             boundary_forcing.ds_depth_coords[f"interface_depth_rho_{direction}"]
@@ -483,11 +469,9 @@ def test_correct_depth_coords_adjusted_for_zeta(
     ],
 )
 def test_correct_depth_coords_zero_zeta(boundary_forcing_fixture, request, use_dask):
-
     boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     for direction in ["south", "east", "north", "west"]:
-
         # Test that uppermost interface coincides with sea surface height
         assert np.allclose(
             boundary_forcing.ds_depth_coords[f"interface_depth_rho_{direction}"]
@@ -512,9 +496,9 @@ def test_computed_missing_optional_fields(
         ), "DOCr should be constant across space and time"
     # 'DOC' was present in the source data and should show spatial or temporal variability
     for direction in ["south", "east", "north", "west"]:
-        assert (
-            ds[f"DOC_{direction}"].std() > 1e-10
-        ), "DOC should vary across space and time"
+        assert ds[f"DOC_{direction}"].std() > 1e-10, (
+            "DOC should vary across space and time"
+        )
 
 
 @pytest.mark.parametrize(
@@ -570,7 +554,6 @@ def test_boundary_forcing_save(boundary_forcing_fixture, request, tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             # Test saving without grouping
             saved_filenames = boundary_forcing.save(filepath, group=False)
 
@@ -601,7 +584,6 @@ def test_boundary_forcing_save(boundary_forcing_fixture, request, tmp_path):
 )
 def test_bgc_boundary_forcing_plot(boundary_forcing_fixture, request):
     """Test plot method."""
-
     bgc_boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     bgc_boundary_forcing.plot(var_name="ALK_south", layer_contours=True)
@@ -619,7 +601,6 @@ def test_bgc_boundary_forcing_plot(boundary_forcing_fixture, request):
 )
 def test_bgc_boundary_forcing_save(boundary_forcing_fixture, tmp_path, request):
     """Test save method."""
-
     bgc_boundary_forcing = request.getfixturevalue(boundary_forcing_fixture)
 
     for file_str in ["test_bf", "test_bf.nc"]:
@@ -628,7 +609,6 @@ def test_bgc_boundary_forcing_save(boundary_forcing_fixture, tmp_path, request):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             # Test saving without partitioning and grouping
             saved_filenames = bgc_boundary_forcing.save(filepath, group=False)
 
@@ -658,8 +638,8 @@ def test_bgc_boundary_forcing_save(boundary_forcing_fixture, tmp_path, request):
 )
 def test_roundtrip_yaml(bdry_forcing_fixture, request, tmp_path, use_dask):
     """Test that creating a BoundaryForcing object, saving its parameters to yaml file,
-    and re-opening yaml file creates the same object."""
-
+    and re-opening yaml file creates the same object.
+    """
     bdry_forcing = request.getfixturevalue(bdry_forcing_fixture)
 
     # Create a temporary filepath using the tmp_path fixture
@@ -668,7 +648,6 @@ def test_roundtrip_yaml(bdry_forcing_fixture, request, tmp_path, use_dask):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         bdry_forcing.to_yaml(filepath)
 
         bdry_forcing_from_file = BoundaryForcing.from_yaml(filepath, use_dask=use_dask)
@@ -680,7 +659,6 @@ def test_roundtrip_yaml(bdry_forcing_fixture, request, tmp_path, use_dask):
 
 
 def test_files_have_same_hash(boundary_forcing, tmp_path, use_dask):
-
     yaml_filepath = tmp_path / "test_yaml_.yaml"
     filepath1 = tmp_path / "test1.nc"
     filepath2 = tmp_path / "test2.nc"
@@ -766,7 +744,6 @@ def test_from_yaml_missing_boundary_forcing(tmp_path, use_dask):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)